The following are my favorites, plus a few. I have them pretty much in order starting with my favorite, but view them all to see for yourself which one you prefer :) You can view my original post about timers too if you are so inclined.
e.ggtimer.com - There's a couple of things I really like about this timer. First, you can actually type in the time you want to use for the timer in the url, for example, e.ggtimer.com/5minutes, would automatically pull up a website with a countdown from 5 minutes. You type in any time amount here, as well as a few other cool things that you learn about on the site's main page.
Teachit Timer - A very large, easy-to-follow output is displayed while the timer is counting down. You use sliders to input the time you would like to set. It also lets you select different final sounds. I really like the visual while the timer is counting down.
Online Stopwatch - This site can serve as a stopwatch or a timer. To use the stopwatch click the green arrow stopwatch link. You'll then be taken to a page that will allow you to start the stopwatch. If you need go back to the main page just click the provided "back" link. To use the timer function of the site, click the "Count Down" red arrow. Use the buttons on the screen to set your time, then click the "Set" button. From here you can start the timer.
timer.onlineclock.net/ - This is a simplistic timer that can be shown quite large on your screen. Just use the links in the upper-left to adjust the size. Use the drop-down menu under the timer to set a time. The timer will begin as soon as a time is selected.
Class Timer - This is a little bit smaller version but it does a great efficient job. It counts up or down depending on the option that you select.
